Transcript ppt - Phenotype RCN

http://phenotypercn.org/
Anatomy Ontologies from a MOD
(Model Organism Database)
perspective
Model Organism Database
(MOD) for Arabidopsis
- focus on genes and their
function
http://phenotypercn.wordpress.com/
21,000 registered users
(9500 updated last 5 years)
Academic researchers:
• grad students
• postdocs
• PIs
Heavy international usage
2010: 1,765,873 visits from 178 countries/territories
http://phenotypercn.wordpress.com/
How does TAIR use phenotype ontologies now?
Plant Ontology
Expression pattern annotation
http://phenotypercn.wordpress.com/
How would we like to use anatomy ontologies?
standardized mutant phenotype descriptions!
http://phenotypercn.wordpress.com/
Why?
search, categorize, compare, infer
Question: Which genes control seed size in Arabidopsis?
Entity:
Flower
Seed
Flowering time
Disease resistance
Drought resistance
Cold tolerance
…
Quality:
Normal size
Decreased size
Increased size
Small
Large
Yellow
Green
Species:
Data type:
Soybean
Tomato
Arabidopsis
Maize
Rice
Sorghum
…
Genes
QTLs
Regulatory networks
Expression
Mutant phenotypes
Images
…
Arabidopsis
genes
Question: Is seed size controlled by the same mechanism in Arabidopsis,
tomato and soybean?
Entity:
Flower
Seed
Flowering time
Disease resistance
Drought resistance
Cold tolerance
…
Quality:
Normal size
Decreased size
Increased size
Small
Large
Yellow
Green
Species:
Data type:
Soybean
Tomato
Arabidopsis
Maize
Rice
Sorghum
…
Genes
QTLs
Regulatory networks
Expression
Mutant phenotypes
Images
…
Soybean
genes
Tomato
genes
Arabidopsis
genes
Question: Which tomato gene can I mutate to give me smaller seeds?
Tomato
phenotype
Tomato
mutant allele
Tomato gene:
may control seed size
>SGN-P669913 (395 Aa)
MDNSNRSYNRNADHLGVNKFGKNINKSPIHQPNFNNANSARQQPQ
PQVYNINKNDFRSVVQQLTGSPSQEPPSKPPQNPSKPPEYEITKD
SATAFDPINRPQIPMHPPAQILAPARPAGGVPYQNNIARPPPHYG
QPSPPMLPPTPGDVWTNTTESPISVYMRYLQNSIIDSGPKQTQFQ
GPGHFQAHPASSGLLPNPSMPPFPSPRXEWPASFPIVAENGPPPP
LLSPRXEWPAASPIARLNGPPPRLLSPRMNGPPLLPSPRMNGPPP
PLPSPGINGPPPLPSPTSQYLLPSPTGFLNLLSPRSPYPLLSPGM
QHPPPLTPNFFFSPMAQPGGFGTGPQFPPSPGYGFPLSPSGFFAM
SSQDGGVNSTTTNRAADLDGFFASSFXPGGRFPSN*
Arabidopsis phenotype:
decreased seed size
Arabidopsis
mutant allele:
iku1-1
Arabidopsis gene:
controls seed size
1
51
101
151
201
251
301
351
401
MDRPRQNDHL
SKNDFRSIVQ
PAVPLPSMAP
VSEYMRYLQS
PGNEQRPYIP
PLQPNQYLPP
SPRYNGFGPL
NFSFSQIAQQ
DY
GVNRIGKNIR
QLTGSPSRES
PQSHPQFARQ
SLGDSGPNAN
GHEQRSYMPA
PGLVPSPVPH
QSPTSQFLQP
GSLGPGAGPS
KSPLHQSTFA
LPRPPQNNSL
PPHQPPFPQT
QMQPGHEQRP
QSQSQSQPQP
NLPSPRFNAP
SPTGYPNMFS
QGPPQPPPSP
ASTSNGAAPR
RPQNTRLQRI
TQQPMMGHRD
YIPGHEQRPY
QPQPQQHMMP
VPVTPTQPSP
PRSPYPLLSP
GLMFPLSPSG
LQTQPQVYNI
RPSPLTQLNR
QFWSNTAESP
VPGNEQQPYM
GPQPRMNMQG
MFSQMYGGFP
GVQYPQPLTP
FFPMPSPRWN
http://phenotypercn.wordpress.com/
What are the barriers?
curation efficiency
funding for curation
lack of interoperability
http://phenotypercn.wordpress.com/
What are the barriers?
curation efficiency
funding for curation
lack of interoperability
reading research articles and
converting data into annotations
is time consuming and expensive!
Current status
Phenotype data in TAIR is still free text
2238 sequenced
genes with free text
phenotypes
Additional 1755
unsequenced mutant
loci with phenotypes
(total of 3993 loci)
4696 images
http://phenotypercn.wordpress.com/
What are the barriers?
curation efficiency / funding (also applies to GO)
- let’s try getting data directly from authors/
funding
lack of interoperability
A
Article Navigator
B
Full Text Frame
C
We crossed syp122-1 to the EMS-induced, null alleles of PEN1,
pen1-1, and pen1-4 (Collins et al., 2003). For both allelic
combinations, the double mutants (identified as described in
Materials and Methods) grew on soil as severely dwarfed plants
with necrotic rosettes (Figure 3, A-E). When plated on MS
medium, double mutant seedlings grew well for the first 2 to 3
wk. Thereafter, necrotic lesions were seen on the rosette
leaves, even though these were propagated in sterile tissue
culture (Figure 3A). The lesions were more frequent under high
light than under low light (compare Figure3C ​with 3D),
suggesting an enhanced susceptibility to oxidative stress. In
spite of their lesions, the double mutants yielded a small
amount of seed and could be propagated as true breeding lines.
Processes requiring polarized secretion such as root hair tip
growth, trichome morphogenesis (Figure 3A), and transmission
through the pollen did not appear to be perturbed in the pen1
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E
Genotype
Ontology Browser
Term: trichome (PO:0000282)
Definition: A unicellular or multicellular plant structure that
forms a non-sclerified outgrowth from the epidermis.
D
Pick Lists
X Selected text
Alleles:
syp122-1
pen1-1
pen1-4
Anatomy:
rosette
seedling
rosette leaf
root hair
trichome
GO:
secretion
trichome morphogenesis
SP term:
dwarf
Maps to:
PATO: height reduced / PO: whole plant
Whole article
Quality:
severe
necrotic
sterile
small
susceptible
Curator-Composed Annotations
Quality
Entity
syp122-1 pen1-1
height reduced
whole plant
syp122-1 pen1-1
necrotic
rosette leaf
2nd term [opt]
Synonym [opt]
dwarf
Add synonym
Add synonym
Add synonym
Vision…
Model organism biologists
Plant breeders
Explore:
Systematists
Leaf Shape Phenotypes
(structured and interoperable)
Ecologists
Adaptation, genetic basis, evolution, effect on yield,
classification, development, gene regulation…